A collection of data files which tries to give support for various chemical MIME types (chemical/*) on Linux/UNIX desktops. Chemical MIME's have been proposed in 1995, though it seems they have never been registered with IANA.

The JChemPaint Applet and Swing Application are Java programs for drawing 2D chemical structures like those found in most chemistry textbooks. It is based on the Chemistry Development Kit (cdk.sf.net). Downloads, tracker, and source code repository can be found on http://jchempaint.github.com

NanoHive is a modular simulator used for modeling the physical world at a nanometer scale. The intended purpose of the simulator is to act as a tool for the study and development of nanotech entities. The project will also focus on the simulation of complex biological applications such as Targeted Drug Delivery by simulating nanowires, magnetic nanoparticles and others. More updates will be added soon.

cclib is an open source library, written in Python, for parsing and interpreting the results of computational chemistry packages. It currently parses output files from ADF, Firefly, GAMESS, GAMESS-UK, Gaussian, Jaguar and ORCA.
IMPORTANT! As of version 1.2, cclib development has moved to github. Please use the flowing pages for up-to-date information about cclib:
Repository (source code, tracker) - https://github.com/cclib/cclib
Online documentation - http://cclib.github.io/

Cca-forum unifies the Common Component Architecture tools and tutorial. It includes the CCA specifications, the Ccaffeine framework for HPC, and related tools. These support multilanguage scientific and parallel computing.

4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.